First , let DS handle it..there are plenty of resources for EI, and the NAPS staff knows what they are doing. It is way to early to be thinking about dropping down.
Second , why did DS get selected for NAPS v. direct Admissions. There is always a reason, and enhanced academic preparation is often it. Pushing a MC is part of the process...the goal isn't to get them through NAPS, its to prepare them for the academic challenges that lay ahead at USNA. Bailing out and taking the easy road now isn't going to help in the long run.
Now for a story ... I was in DS' shoes 40 years ago. I don't know what the NAPS curriculum is now, but back in the day we had two Math Classes...and I got placed in high track, and literally got my A$$ kicked in both. My average was below 60 in both classes when I went home for Christmas,: my parents arranged a tutor over Christmas break and I still didn't catch on. I was doing weekly visits with the NAPS CO , who was encouraging and certainly recognized my efforts, but I was still getting kicked. Finally, just after the third trimester or reporting period stop, the powers to be moved me to middle track, where I was essentially retaking material that I had learned and failed before, and the light bulb clicked on. I graduated from NAPS, and did pretty well at USNA (close to top 10%). I credit NAPS for teaching me how to learn, and that wouldn't have happened if I had gotten moved down to middle track early in the program.,
Bottom line ..this is DS struggle, not yours. Encourage him to show the work ethic and make the effort that makes the NAPS faculty want to see him succeed, and communicate with his Chain of Command. It may be tough, but he'll make it.
Good luck.